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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttagctaatctcctgcctataatgtctgcctcacaagaaggttgttgggttttgttcaagaatgctaatcaagacttgcatttctctgggacaatgcagATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATATCATTGAAACTGGGAACAGTGAGACGTTTCTTCAAAAGGCAATTCAGGAG

Basic information

species Physcomitrella patens
transcript PP1S98_68V6.1
intron # 1
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208373647|gb|DC952472.1|DC952472
EST:     ACCCTTAGGCAGAAAATGATGGAAGAATATAAGGAGACTGTGGAACGGAG                         ATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATAT
genomic: ACCCTTAGGCAGAAAATGATGGAAGAATATAAGGAGACTGTGGAACGGAGgtgagcatta ... gacaatgcagATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATAT
EST: gi|100415492|gb|BY992869.1|BY992869
EST:     ACCCTTAGGCAGAANATGATGGGAGAATATAAGGAGACTGTGGGACGGAG                         ATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATAT
genomic: ACCCTTAGGCAGAAAATGATGGAAGAATATAAGGAGACTGTGGAACGGAGgtgagcatta ... gacaatgcagATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATAT
EST: gi|162228781|gb|FC405809.1|FC405809
EST:     ACCCTTAGGCAGAAAATGATGGAAGAATATAAGGAGACTGTGGAACGGAG                         ATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATAT
genomic: ACCCTTAGGCAGAAAATGATGGAAGAATATAAGGAGACTGTGGAACGGAGgtgagcatta ... gacaatgcagATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATAT
EST: gi|37826966|gb|BJ584978.1|BJ584978
EST:     CCCTTAGGCAGAAAATGATGGAAGAATATAAGGAGACTGTGGAACGGAG                         ATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATAT
genomic: CCCTTAGGCAGAAAATGATGGAAGAATATAAGGAGACTGTGGAACGGAGgtgagcatta ... gacaatgcagATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATAT
EST: gi|208351081|gb|DC926002.1|DC926002
EST:     A-CCTTAGGCAGAAAATGATGGAAGAATATAAGGAGACTGTGGAACGGAG                         ATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATAT
genomic: ACCCTTAGGCAGAAAATGATGGAAGAATATAAGGAGACTGTGGAACGGAGgtgagcatta ... gacaatgcagATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 9 (upstream exon), 35 (downstream exon)
Score: 6

TCACGGGCACGCTGAGAAAGAAGCTTAAGGATCTCATGGGGGAATTTCAAACCCTTAGGCAGAAAATGATGGAAGAATATAAGGAGACTGTGGAACGGAGgtgagcatta ... gacaatgcagATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATATCATTGAAACTGGGAACAGTGAGACGTTTCTTCAAAAGGCAATTCAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggttttgttcaagaatgctaatcaagacttgcatttctctgggacaatgcagATATTACACAGTAACTGGTGAGCATGCGGATGATGACACTATAGAACATATCATTGAAACTGGGAACAGTGAGACGTTTCTTCAAAAGGCAATTCAGGAG
                  tgctaat  putative branch site (score: 6)
     ttttgtt  TA-rich tract